Contacts of the strand formed by residues 306 - 314 (chain B) in PDB entry 3UAJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B CYS* 3.6 25.8 - - + -
304B GLY 3.9 10.5 - - - -
305B LYS* 1.3 83.2 - - - +
307B SER* 1.3 59.9 + - - +
324B VAL* 4.0 22.4 - - + -
325B LYS 3.4 15.3 - - - -
326B TYR* 3.4 41.5 - + + -
327B GLU* 5.0 0.9 - - - -
335B VAL* 3.6 25.8 - - + -
336B PRO* 3.9 10.8 - - + -
358B ALA* 4.6 5.4 - - + -
365B THR* 5.8 2.0 - - - -
380B ILE* 4.0 25.0 + - + +
381B GLY* 4.3 15.0 - - - -
385B SER 5.1 2.5 + - - +
386B ALA* 6.2 0.2 - - - +
387B LEU* 3.5 25.8 + - + +
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LYS* 6.0 2.2 - - - -
306B PHE* 1.3 75.1 - - - +
308B ILE* 1.3 64.4 + - - +
309B ASP 3.3 0.3 + - - -
324B VAL* 3.4 4.6 - - - -
325B LYS* 2.8 50.3 + - - +
327B GLU* 2.8 26.5 + - - -
387B LEU* 4.6 6.7 - - - -
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER* 1.3 70.7 - - - +
309B ASP* 1.3 64.2 + - - +
310B LYS 3.4 4.7 - - - +
311B GLU* 4.7 23.6 - - + +
322B VAL* 3.9 15.3 - - + -
323B LYS 3.5 3.4 - - - +
324B VAL* 3.8 15.7 - - + -
387B LEU* 3.8 27.8 - - + +
389B LEU* 3.9 28.0 - - + -
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Residues in contact with ASP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER 3.3 4.0 + - - -
308B ILE* 1.3 72.4 - - - +
310B LYS* 1.3 58.6 + - - +
323B LYS* 2.8 21.8 + - + +
324B VAL 4.5 0.7 - - - +
325B LYS* 4.7 16.3 - - + +
364B VAL* 3.5 43.2 - - + +
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 3.5 68.4 + - + +
105A CYS 4.5 4.9 + - - -
106A GLY* 5.1 8.3 - - - -
308B ILE* 4.2 5.4 - - - +
309B ASP* 1.3 80.0 - - - +
311B GLU* 1.3 67.5 + - - +
322B VAL* 3.7 5.5 - - - +
323B LYS* 3.5 44.6 + - + +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 3.8 15.6 - - - -
106A GLY 5.5 0.7 - - - +
308B ILE* 4.7 19.1 - - + +
310B LYS* 1.3 77.8 - - - +
312B MET* 1.3 77.0 + - - +
313B ALA* 3.4 5.5 + - - +
389B LEU* 5.8 5.2 - - + -
391B TRP* 5.2 4.2 - - - -
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Residues in contact with MET 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 5.7 0.3 - - - +
308B ILE* 5.7 0.2 - - - +
310B LYS 3.7 1.6 + - - -
311B GLU* 1.3 84.3 - - - +
313B ALA* 1.3 60.9 + - - +
320B THR* 3.8 27.4 - - + +
321B VAL 3.4 13.7 - - - +
322B VAL* 3.8 21.9 - - + +
369B LEU* 3.9 21.1 - - - -
378B ILE* 3.8 28.5 - - + -
389B LEU* 4.9 23.1 - - + +
390B HIS 5.1 0.9 - - - +
391B TRP* 3.5 53.9 - - + -
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TRP* 4.4 2.9 - - + +
106A GLY 3.9 21.8 - - - +
107A LEU* 3.9 17.9 - - + -
108A PHE* 4.1 20.3 - - + -
311B GLU 3.4 6.2 + - - +
312B MET* 1.3 73.5 - - - +
314B GLU* 1.3 61.1 + - - +
315B THR 3.9 0.2 + - - -
320B THR* 3.4 2.9 - - - -
321B VAL* 3.0 33.2 + - - +
391B TRP* 4.4 4.9 - - - -
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.7 6.9 - - + +
108A PHE* 3.6 23.7 + - - +
313B ALA* 1.3 72.8 - - - +
315B THR* 1.3 73.4 + - - +
318B GLY* 3.6 27.0 - - - +
319B THR 3.6 3.1 - - - +
320B THR* 4.0 5.6 - - + -
391B TRP* 3.6 29.5 + - + -
392B PHE 4.6 0.7 - - - +
393B ARG* 3.5 30.2 - - - +
394B LYS* 4.7 20.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il